# Genome-wide identification and characterization of DCL, AGO and RDR gene families in sister mangrove species Kandelia obovata and Kandelia candel

## TL;DR

This study compares gene families involved in plant defense and stress response between two mangrove species, identifying genes linked to cold tolerance in Kandelia obovata.

## Contribution

First genome-wide comparison of AGO, DCL, and RDR gene families in Kandelia obovata and Kandelia candel, revealing subfamily expansions and stress-related genes.

## Key findings

- K. obovata has 8 AGO genes while K. candel has 6, suggesting subfamily expansion.
- Certain genes in K. obovata show high expression under stress conditions, indicating roles in stress response.
- Promoter and 3D structure analyses suggest reasons for K. obovata's greater cold tolerance.

## Abstract

The AGO, DCL and RDR gene families work together in the plant gene silencing process, playing crucial roles in regulating gene expression, responding to stress, and gene silencing, thus forming an essential part of the plant's defense system. In this study, we systematically identified and characterized these genes in the closely related mangrove species Kandelia obovata and Kandelia candel. We found a total of 8/6 AGO, 4/3 DCL and 5/4 RDR genes in these species, respectively. Phylogenetic analysis classified them into 3, 4, and 4 subfamilies correspondingly. Comparing with the sister species K. candel helped clarify key genes involved in cold tolerance. Each gene exhibited different expression levels across various tissues and stress conditions, with certain genes showing notably high expression. Furthermore, analyses of promoters, protein interaction networks, and three-dimensional structures provided deeper insights into the possible reasons behind the greater cold tolerance of K. obovata compared to K. candel. These comprehensive results offer a theoretical basis for further experimental validation of the specific roles of these genes in K. obovata's stress resistance and for investigating gene-environment interactions.

•First K. obovata-K. candel AGO/DCL/RDR genome comparison.•Compare to K. candel, K. obovata subfamily expansions.•Some gene are crucial for K. obovata stress response.

First K. obovata-K. candel AGO/DCL/RDR genome comparison.

Compare to K. candel, K. obovata subfamily expansions.

Some gene are crucial for K. obovata stress response.